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jodyphelan/portugal-microbiome-setup.sh

Last active July 4, 2023 20:11
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portugal-microbiome-setup.sh
# mamba create -n tb-profiler python bwa "samtools>=1.12" "bcftools>=1.12" requests snpEff samclip trimmomatic parallel "delly>=0.8.7" "freebayes>=1.3.5" tqdm bedtools jinja2 filelock docxtpl
wget -O pathogen-genomics-microbiome-profiler-spec.txt https://gist.githubusercontent.com/jodyphelan/92d8a63f498434f1c30bd48fcff8f8bb/raw/79d24bc7dcc72589145fbb5079ad108fe7fd51f7/microbiome-spec.txt
conda create --file pathogen-genomics-microbiome-profiler-spec.txt --name microbiome
conda activate microbiome
pip install multiqc
mv Module6 Module6_old
mkdir Module6
cd Module6
wget -O microbiome_data.tgz --no-check-certificate https://tbdr.lshtm.ac.uk/static/microbiome_data.tgz
tar -xvf microbiome_data.tgz
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